Alaksa, 1) What rmsd / sigma are you contouring your density at ? i.e. are you down in the "noise" or are you at a reasonable value for your Fo-Fc map?
2) It looks like some of your side-chains appear to have more than one conformation - it's fairly easy in Coot to position and model both. Tony. --- Mobile Account --- On 26 Apr 2012, at 21:55, "Alaksa" <[email protected]> wrote: > > Dear all > I am refining the crystal structure of a protein (Rfree and Rvalue are <25 > and <20 A respectively). However, I am getting the negative density at some > places in the side chain of residues. All side chains are properly fitting > into the blue density, however red density blobs are also present at the same > place along with blue density . At some other place this red density is also > present in the main chain along with blue density (see the attached snaps). > If I have mutate the residues to alanine then density becomes blue, but when > change into the original residue, after refmac5 again it is showing red blob. > Also if I rotate the chain to place it in green density, but after running > refmac it attain original position having red blob. I am not using TLS. > I am seeking some strategy so that the problem can be solved. Please suggest > me the possible reasons and remedy. Also i am naive in crystallography. > > Thanks > Alaksa > > > <coot2.png> > <coot1.png> > <coot3.png> > <coot4.png>
